More intelligent determination of index file path

Treat URLs with query strings properly, add index extension to the path element not just the end of the string

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1600 8bce386e-0d6e-43e0-b1ca-608082c0432d
Have TabixReader use buffered seekable streams.

Also allow TabixReader to take an index file as an input parameter, instead of just adding an extension. This is necessary for URLs with query parameters.

Add additional ISeekableStreamFactory methods. 


git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1601 8bce386e-0d6e-43e0-b1ca-608082c0432d
Move appendToPath to ParsingUtils

Add isRemoteURL and isURL to HttpUtils, have it treat URLs more intelligently

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1602 8bce386e-0d6e-43e0-b1ca-608082c0432d
Merge remote-tracking branch 'upstream'